Dear users, As Suggested by Erik, I used g_hbond with -contact to obtain a matrix of each contact as a function of time. I used the following command - g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e 4400 -hbn c.ndx
I get only three contacts in the index file. The protein is a dimer of 474 residues (237 each). With a distance cut off of 0.5nm there should have been more number of contacts. And what is the difference in using -r only or -r2 only and combining -r and -r2? Thank you Kavya On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M <hmkv...@gmail.com> wrote: > Thank you! > > > On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund <er...@xray.bmc.uu.se>wrote: > >> Perhaps g_hbond -contact will do what you want. >> >> Erik >> >> >> On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: >> >> Dear users, >>> >>> How can I get the number of interactions of each residue >>> within a cut off as a function of time. just like g_saltbr writes >>> with the option -sep. >>> I tried using g_mdmat but it gives an average contact map. >>> >>> Thank you >>> Kavya >>> -- gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read >>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use thewww >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
